"The Musical Matrix of the Universe" by Paul Re

Select publications by Dr. Coutsias

  1. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics Evangelos Coutsias, Katrina Lexa, Michael Wester, Sara Pollock and Matt Jacobson 10.1021/acs.jctc.6b00250, Journal of Chemical Theory and Computation (2016).
  2. Accurate de novo design of hyperstable constrained peptides, Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V.S.R.K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin1, Yifan Song, Thomas W. Linsky, Andrew Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, and David Baker (accepted) Nature (2016).
  3. Constraint methods that accelerate free-energy simulations of biomolecules Alberto Perez, Justin L. MacCallum, Evangelos A. Coutsias and Ken A. Dill (accepted) Journal of Chemical Physics (2015).
  4. A human transcription factor in search mode K. Hauser,B. Essuman,Y. He,E. Coutsias, M. Garcia-Diaz and C. Simmerling Nucleic Acids Research (2015) doi: 10.1093/nar/gkv1091. Supplementary Materials
  5. On the comparison of energy sources: Feasibility of radio frequency and ambient light harvesting Alexander O. Korotkevich, Zhanna S. Galochkina, Olga Lavrova, Evangelos A. Coutsias, doi:10.1016/j.renene.2015.03.065 Renewable Energy 2015, 81, 804-807.
  6. Flexibility of Bricard's linkages and other structures via resultants and computer algebra Robert H. Lewis and Evangelos A. Coutsias, doi:10.1016/j.matcom.2014.11.002 Mathematics and Computers in Simulation 125 (2016), 152 - 167 (arXiv preprint arXiv:1408.6247, 2014).
  7. Selective Inhibition of Initiator versus Executioner Caspases Using Small Peptides Containing Unnatural Amino Acids Chris J. Vickers, Gonzalo E. González-Páez, Kevin M. Litwin, Jeffrey C. Umotoy, Evangelos A. Coutsias, and Dennis W. Wolan, dx.doi.org/10.1021/cb5004256 | ACS Chem. Biol. 2014, 9(10), 2194-2198.
  8. The FALC-Loop web server for protein loop modeling Junsu Ko, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Julian Lee and Chaok Seok, Nucleic Acids Research, 39, W210-W214 (2011), doi:10.1093/nar/gkr352
  9. Assessing protein loop flexibility by hierarchical Monte Carlo sampling Jerome Nilmeier, Lan Hua, Evangelos A. Coutsias and Matt P. Jacobson, J. Chem. Theory Comput., 7(5), 1564-1574, (2011). DOI: 10.1021/ct1006696.
  10. Protein loop modeling by using fragment assembly and analytical loop closure Julian Lee, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias and Chaok Seok, PROTEINS: Structure, Function, and Bioinformatics, 78(16), 3428-3436, Dec. 2010 ( published online: 9/24/10 ), DOI: 10.1002/prot.22849,
  11. Topology of Cyclooctane Energy Landscape Shawn Martin, Aidan Thompson, Evangelos A. Coutsias and Jean-Paul Watson, JChemPhys 132, 234115 (2010) ( published online: 6/21/10 ), DOI: 10.1063/1.3445267, Supplementary Materials
  12. Sub-Angstrom Accuracy in Protein Loop Reconstruction by Robotics-Inspired Conformational Sampling Daniel J. Mandell, Evangelos A. Coutsias and Tanja Kortemme, Nature Methods 6, 551 - 552 (2009); doi:10.1038/nmeth0809-551 Supplementary Materials
  13. Delay-induced destabilization of entrainment of nerve impulses on ephaptically coupled nerve fibers M.H. Adhikari, J.K. McIver, E.A. Coutsias, Physical Review E 79, 011910 (2009) (8 pages), DOI: 10.1103/PhysRevE.79.011910 (accepted, 12/16/2008).
  14. Periodic Solutions of a Singularly Perturbed Differential Delay Equation M.H. Adhikari, E.A. Coutsias, J.K. McIver, Physica D, 237(24), pp.3307-3321, (Dec. 15, 2008), doi:10.1016/j.physd.2008.07.019 .
  15. Algorithmic Dimensionality Reduction for Molecular Structure Analysis, W.M. Brown, S. Martin, S.N. Pollock, E.A. Coutsias, J.P. Watson, J. Chem. Phys. 129(6), 064118(pp.1-13) (2008) DOI: 10.1063/1.2968610 (web release, 8/14/2008).
  16. Scaffold Topologies I: Exhaustive Enumeration up to Eight Rings, S.N. Pollock, E.A. Coutsias, M.J. Wester and T.I. Oprea, J. Chemical Information and Modeling, 2008 (Jul. 8), 48(7), 1304-1310, DOI:10.1021/ci7003412 (web release 7/8/2008).
  17. Scaffold Topologies II: Analysis of Chemical Databases, M.J. Wester, S.N. Pollock, E.A. Coutsias, T.K. Allu, S. Muresan and T.I. Oprea, J. Chemical Information and Modeling, 2008 (Jul. 8), 48(7), 1311-1324, DOI:10.1021/ci700342h, (web release, 7/8/2008).
  18. Iterative assembly of helical proteins by optimal hydrophobic packing, A.Wu, E.A. Coutsias and K.A. Dill, Structure, 16, 1257-1266, August 6, 2008.
  19. Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules Chaok Seok and E.A. Coutsias, Bulletin of the Korean Chemical Society, 28(10), p.1705-1708, (2007).
  20. Algorithmic Search for Flexibility using Resultants of Polynomial Systems. Robert H. Lewis and E. A. Coutsias, pp. 68-79. Automated Deduction in Geometry: 6th International Workshop, Pontevedra Spain, August 31- September 2, 2006, Revised Papers. Series: Lecture Notes in Computer Science , Vol. 4869 Sublibrary: Lecture Notes in Artificial Intelligence Botana, Francisco; Recio, Tomas (Eds.) Springer, Berlin, 2007.
  21. Spectral element modeling of semiconductor heterostructures Greg von Winckel, S. Krishna, E.A. Coutsias. (Mathematical and Computer Modeling, Volume 43, Issues 5-6, Pages 582-591 (March 2006))
  22. Resultants and Loop Closure E.A. Coutsias, C. Seok, M.J. Wester and K.A. Dill. (International Journal of Quantum Chemistry, 106(1), 176-189, 2006)
  23. Rotational Superposition and least squares: The SVD and Quaternions approaches yield identical results. E.A. Coutsias, C. Seok, K. Dill. Journal of Computational Chemistry Volume 26, Issue 15, Date: 30 November 2005, Pages: 1663-1665
  24. A reduced-order partial differential equation model for dynamics of the flow in a thermosyphon. Elisabeth Burroughs, E.A. Coutsias, L. Romero. (Journal of Fluid Mechanics, 543, 203-237, 2005)
  25. Research Results on Biomagnetic Imaging of Lung Tumors. Laurel O. Sillerud, Popa, S.G., Coutsias, E.A., Sheltraw, D., Kuethe, D., Adolphi, N. Proc. SPIE Vol. 5692, p. 1-10, Advanced Biomedical and Clinical Diagnostic Systems III; Tuan Vo-Dinh, Warren S. Grundfest M.D., David A. Benaron M.D., Gerald E. Cohn; Eds., April 2005
  26. The flexibility in the proline ring couples to the protein backbone. Bosco Ho, E.A. Coutsias, C. Seok, K. Dill (Protein Science, 2005, 14:1011-1018) proline.m , matlab script for computing proline conformations for given phi angle.
  27. Using Quaternions to calculate RMSD E.A. Coutsias, C. Seok, K.A. Dill (Journal of Computational Chemistry, 2004, vol 25, pp 1849-1857)
  28. Notes on the Quaternions, E.A. Coutsias, L. Romero (Sandia Technical Report, SAND2004-0153, 2004).
  29. A Kinematic View of Loop Closure (pdf), E.A. Coutsias, Chaok Seok, M.P. Jacobson, K.A. Dill (Journal of Computational Chemistry, Volume 25, Issue 4, pp 510 - 528 (2004) ) _Biocomp04 presentation (ppt)
  30. Invertibilty of Current Density from Near-Field Electromagnetic Data Daniel Sheltraw, E.A. Coutsias, (2003, Journal of Applied Physics, v94, n8, pp. 5307-5315).
  31. Thin-Section CT Evidence of Bronchial Thickening in Children with Stable Asthma: Bronchoconstriction or Airway Remodeling? Loren Ketai, Cecilia Coutsias, Susan Williamson and Evangelos Coutsias (Academic Radiology 2001; 8:257-264) Supplementary materials
  32. Two-Dimensional Turbulence in Square and Circular Domains with No-Slip Walls Hermann Clercx, A.H. Nielsen, D.J. Torres, E.A. Coutsias. ( Eur.J.Mech. B-Fluids 20(2001) 557-576).
  33. The Dynamics of Forced Circular Shear Layers Keith Bergeron, E.A. Coutsias, J.P. Lynov, A.H. Nielsen. ( Journal of Fluid Mechanics, 402, pp.255-289, 2000). ANNULUS picture gallery
  34. An accurate and efficient spectral method for studies of the dynamical properties of forced, circular shear layers, J.P. Lynov, K. Bergeron, E.A. Coutsias and A.H Nielsen, Applied Numerical Mathematics, 33, p.175-181, (2000).
  35. Pseudospectral Solution of the 2D Navier-Stokes Equations in a Disk David J. Torres, E.A. Coutsias, SIAM Journal of Scientific Computing, 21, pp 378-403, (1999). Disk picture gallery
  36. Decaying Two-Dimensional Turbulence in Bounded Flows Anders H. Nielsen, D.J. Torres, E.A. Coutsias. (25th EPS Conf. on Controlled Fusion and Plasma Phys., 1998).
  37. The Approximate Functional Formula for the Theta Function and Diophantine Gauss Sums ( Transactions of the AMS, 350(2), pp.615-641, 1998) E.A. Coutsias, N.D. Kazarinoff.
  38. A Nucleation Theory of Cell Surface Capping E.A. Coutsias, M.J. Wester, A.S. Perelson. Journal of Statistical Physics, 87(5/6), 1179 - 1203, (1997).
  39. Optimized Preparation of Quantum States by Conditional Measurements Gershon Kurizki, M. Harrel, J.K. McIver, E.A. Coutsias. Phys. Rev. A, 53(6), 4534 - 4538, (1996).
  40. Self Organization in 2D Circular Shear Layers, K. Bergeron, E.A. Coutsias, J.P. Lynov and A.H. Nielsen. Physica Scripta T67, 1996, p. 33-37.
  41. An Efficient Spectral Method for Ordinary Differential Equations with Rational Function Coefficients E.A. Coutsias, T. Hagstrom, D.J. Torres. Mathematics of Computation 65, 611 - 635, (1996).
  42. Integration Preconditioners for Differential Operators in Spectral tau Methods E.A. Coutsias, T. Hagstrom, J.S. Hesthaven, D.J. Torres. ( ICOSAHOM 3, 1995; p.21-38 / Spec. Issue Houston Journal of Mathematics - 1996)
  43. An Accurate and Efficient Spectral tau Method for the Incompressible Navier-Stokes Equations in a Planar Channel E.A. Coutsias, J.S. Hesthaven, J.P. Lynov. (ICOSAHOM 3, 1995; p.39-54 / Spec. Issue Houston Journal of Mathematics - 1996) CHANNEL picture gallery
  44. Acoustic Wave nonlinearity in stimulated Brillouin scattering, Bruce S. Masson, E.A. Coutsias. (J.Opt.Soc.Am., B, 1367-1373, (1994)).
  45. Vortex Dipoles Colliding with Curved Walls, E.A. Coutsias, J.P. Lynov, A.H. Nielsen, M. Nielsen, J.Juul Rasmusen and B. Stenum. in Proc. of ``Future Directions in Physical and Biological Systems'', Lyngby, Denmark, P.L. Christiansen, J.C. Eilbeck, and R.D. Parmentier, eds., Plenum Press, New York, 51-54, (1992).
  46. Coherent Vortical Structures in Two-Dimensional Plasma Turbulence Hans Pecseli, E.A. Coutsias et al. (Plasma Physics and Controlled Fusion - 34(13), p.2065-2070, (1992)).
  47. Fundamental interactions of vortical structures with boundary layers in two-dimensional flows E.A. Coutsias, J.P. Lynov. (Physica D51, 482-497, (1991)).
  48. A new Formulation for Dendritic Crystal Growth in Two Space Dimensions E.A. Coutsias, H. Segur.
  49. ( in "Asymptotics beyond All Orders", H. Segur, H. Levin and S. Tanveer, Eds., Plenum Press, New York, 1991, pp. 87-104)
  50. Spectral methods for numerical plasma simulation, E.A. Coutsias, F.R. Hansen, T. Huld, G. Knorr and J.P. Lynov. Physica Scripta, 40, 270-279, (1989).
  51. Caustics and virtual cathodes in electron beams E.A. Coutsias. (J. Plasma Phys., 40(2), 369-384, (1988)).
  52. Disorder, renormalizability, theta functions and cornu spirals E.A. Coutsias, N.D. Kazarinoff. (Physica, 26D, 295-310, (1987)).
  53. A moving boundary model of acrosomal elongation, Alan S. Perelson and E.A. Coutsias. J. Math. Biology, 23, 361-379, (1986).
  54. Non relativistic Kapitza-Dirac scattering E.A. Coutsias, J.K. McIver. (Phys. Rev. A, 31, 3155-3168, (1985)).
  55. Effects of thermal spread on the space charge limit of an electron beam E.A. Coutsias. (J. Plasma Phys., 31, 313-320, (1984)).
  56. The aging of nuclei in a binary mixture E.A. Coutsias, J.C. Neu. (Physica, 12 D, 295-302, (1984)).
  57. E.A. Coutsias, D.J. Sullivan. Space charge limit instabilities in electron beams (Phys. Rev. A, 27, 1535, (1983)).
  58. Long-time behavior of Ginzburg-Landau systems far from equilibrium E.A. Coutsias, B. Huberman. (Physical Rev. B, 24, 2592, (1981)).
  59. On an application of perturbation methods to the Beam-Beam Interaction, T. Bountis and E.A. Coutsias. in Proceedings of the Symposium on Nonlinear Dynamics and the Beam-Beam Interaction, March 19-21,1979, E. Herrera and M. Month, eds., APS, Brookhaven National Laboratory, 53-61, (l980).
  60. Stable oscillations in single species growth models with hereditary effects, Donald S. Cohen, E.A. Coutsias and J.C. Neu. Mathematical Biosciences, 44, 255-268, (1979).

  • (ca. 1913)

  • Raoul Bricard: Memoir on the theory of the articulated octahedron
  • (English translation from the French (1897) original )

  • Current work. Last edit: Tue Dec 16 21:31:35 MST 2008

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